The blaze, which started late Tuesday, sent powerful blasts into the night sky and the exploding ordnance shook buildings miles away.
"I would like to tell my compatriots that the situation is under control and to remain calm," President Mahamat Idriss Deby Itno told the press during a visit to the site of the explosion.
"This is not the first time there have been explosions of ammunition shops. This should teach us lessons, so that from now on we can no longer build shops in the middle of the city", Deby said.
Health Minister Abdelmadjid Abderahim told journalists the death toll would probably rise as many of the 46 injured were in an "extremely serious" condition.
Unexploded shells and other munitions could be seen scattered on the ground Wednesday amid the burned-out wreckage of military vehicles.
Government spokesman Abderaman Koulamallah said the cause was not "criminal" but an investigation was under way.
- Burned -
The sky was lit up by flames above the Goudji area -- where the army's largest depot of ammunition is located -- for several hours before tapering off and finally ceasing after midnight.
Explosions shook buildings up to seven kilometres (four miles) away and the flames were visible from far off.
"The roof of our house was blown off by one of the explosions," said Kadidja Dakou, who lives in the Amsinene area near Goudji.
The 36-year-old and her three children took refuge in the street alongside their neighbours, fearing their houses would collapse, she told AFP.
"The soldiers had time to evacuate the vehicles, heavy weapons etc. and were able themselves to take shelter," Koulamallah said.
Nearby, gutted buildings could be seen and at least one huge crater was visible in the grounds of the military camp.
"I call on people to remain calm and serene and to avoid handling any object that may have landed," Regional Planning Minister Mahamat Assileck Halata Assileck said, adding deminers were at work.
During the night, the president offered his condolences to victims' families.
The grieving family of a six-year-old girl sat in front of ruined houses in Amsinene after a shell fell in the room of the child, killing her, the family told AFP.
"She burned to death, we couldn't get her out" of the house, her cousin, who did not want to be named, said.
- Iron fist -
Authorities cordoned off the area with a heavy security presence, where thick red smoke hung in the air long after the blasts stopped.
There are multiple homes in the neighbourhood that is the site of the depot, which lies near the international airport and a base where French troops are stationed.
The blaze "caused explosions of ammunition of all calibres", an official with the French forces told AFP on condition of anonymity. He said no French casualties had been reported.
Chad, one of the world's poorest nations, is considered vital in the fight to stop the march of jihadists through the Sahel region.
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